add interactive_rstudio_0_3.xml

tools/interactive/interactive_rstudio_0_3.xml

@@ -0,0 +1,65 @@
+<tool id="interactive_tool_rstudio" tool_type="interactive" name="RStudio" version="0.3" profile="22.01">
+    <description>integrated development environment for R</description>
+    <requirements>
+        <container type="docker">quay.io/galaxy/docker-rstudio-notebook:23.1</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="RStudio" requires_domain="True">
+            <port>8787</port>
+            <url>/</url>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
+        <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
+        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
+        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
+        <environment_variable name="DEBUG">true</environment_variable>
+        <environment_variable name="DISABLE_AUTH">true</environment_variable>
+        <environment_variable name="API_KEY" inject="api_key" />
+    </environment_variables>
+    <command><![CDATA[
+        #import re
+        export GALAXY_WORKING_DIR=`pwd` &&
+        mkdir -p ./rstudio/outputs/ &&
+        mkdir -p ./rstudio/data &&
+
+        ## change into the directory where the notebooks are located
+        cd ./rstudio/ &&
+
+        ##sed -i 's|/monitor.*||g' /etc/services.d/nginx/run &&
+        ##/etc/init.d/syslog-ng start &&
+        /init &
+        ##rstudio-server start &&
+        sleep 5 &&
+        chmod 777 /tmp -R &&
+        tail -f /var/log/rstudio-server/rserver.log
+    ]]>
+    </command>
+    <inputs>
+        <!--<param name="input" type="data" optional="true" label="Include data into the environment"/>-->
+    </inputs>
+    <outputs>
+        <data name="jupyter_notebook" format="ipynb" label=""></data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="mode" value="previous" />
+            <param name="ipynb" value="test.ipynb" />
+            <param name="run_it" value="true" />
+            <output name="jupyter_notebook" file="test.ipynb" ftype="ipynb"/>
+        </test>
+    </tests>
+    <help>
+    This familiar R analysis software suite will let you explore your
+    datasets in depth. Comes with ggplot2, RODBC, maps, shinyapps, knitr,
+    LaTeX, bioconductor, cummeRbund, and many more pre-installed packages.
+
+    Galaxy offers you to use RStudio directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
+    do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in RStudio.
+
+    The convenience functions gx_put() and gx_get() are available to you to interact with your current Galaxy history. You can save your workspace with gx_save().
+
+    For example, gx_get(42) will fetch dataset 42 from your history and return the file location
+    </help>
+</tool>